Basics of X-Area for image plates

Transcription

1 Basics of X-Area for image plates Commercial software to process single-crystal and powder x-ray data from STOE image plates and PILATUS detectors Andrzej Grzechnik 1 & Karen Friese 2 1 Institute of Crystallography, RWTH Aachen, Germany 2 Jülich Centre for Neutron Science, Jülich, Germany grzechnik@xtal.rwth-aachen.de

2 Crystallographic problems that X-Area handles without any problems twinning modulated structures composites polytypism high-pressure data

3 Crystallographic problems that X-Area handles without any problems twinning modulated structures composites polytypism high-pressure data

4 = 0-180º, φ = 0-360º, χ = 45º, 2 = 0, 15, 30, 45, 60º ~220 mm 2 = 58º The diameter of the image plate of 340 mm 2 = 0º IPDS-2T (STOE) Mo-Ka

5 Peak search Indexing in reciprocal space

6 Using the currently selected peaks all difference vectors between all peak positions are calculated, normalised, and projected onto the horizontal plane of the Ewald sphere. When the crystal is a true single crystal, a series of sharp lines can be seen. Each pixel represents a direction in the reciprocal space. The picture is colour coded, the brighter the pixel the larger the frequency of difference vectors in that direction. Each line corresponds to a set of parallel, equally spaced layers in the reciprocal space. In the case of the high-pressure data, the lines from the crystal, two diamonds, and grainy spots of the gasket rings are superimposed.

7 The diamond orientation matrices are useful to check the alignment. They could be used for any other measurements in the same DAC. Hence, it is enough to find them once. Two diamond matrices cf, a 7.1 Å A contamination by the "half-wavelength" component of the Mo spectrum from a tube Diamond l/2 reflections both in a crystal-monochromated beam and in a filtered beam.

8 Twins

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10 Shading masks

11 Masking the shaded areas of the detector (each frame has its own mask) The masks could be re-used for any other data collected in the same DAC. Hence, it is enough to determine them once. The strong diamond reflections could be masked this way.

12 Integration

13 Shading cone instead of masks

14 The coordinate system uvw is centered on the goniomter: the vector v is directing upwards vertically, w is directing to the centre of the collimator, and u is oriented in a way that a righthanded Cartesian coordinate system is built. The cone is defined by the vector relating the position of the DAC with respect to the direct beam and the opening angle. When the DAC is perpendicular to the beam at = 0, j = 0, and = 0, the vector is (1 0 0). For j = 90, it is (-1 1 0). The reflections marked in grey on the following picture are the ones that are outside of the cone.

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16 Integration masks Elliptical masks are used to integrate peak and background intensities. For each mask the smallest diameter is given by W = A + B tanθ, the largest diameter is defined by W / cos(2θ) + Δλ/λ tanθ (oblique incidence at higher 2θ angles and a1-a2 splitting). For obtaining the peak intensity the inner area of the mask is used. For determining the background, the pixels at the border of the ellipse are taken. EMS means effective mosaic spread and combines the divergence of the primary beam with the mosaic spread of a crystal. For a given instrument setup (the X-ray source, monochromator, and collimator) the beam divergence is constant. However the mosaic spread varies from crystal to crystal, so that EMS should be determined for each measured crystal. EMS determines how long a reflection is in the reflecting position when it passes through the surface of the Ewald sphere. The default parameters are A = 14, B = 4, and EMS = 0.01

17 Automatic optimization of A, B, and EMS: multiple frames 3-7 It is a very tricky procedure in the case of large overlap of crystal reflections with diamond reflections and gasket rings. You can t use it without having a proper cone or masks for shaded areas of the detector. You should never fully trust what this procedure gives you. Visual inspection of the results is imperative.

18 Automatic optimization of A, B, and EMS: searching for the lowest R int It is a very tricky procedure in the case of large overlap of crystal reflections with diamond reflections and gasket rings. You can t use it without having a proper cone or masks for shaded areas of the detector. You should never fully trust what this procedure gives you. Visual inspection of the results is imperative.

19 Simulation of the integration masks Usually the A, B, and EMS parameters for a good crystal of an inorganic solid in a DAC hardly ever are larger than 20, 6, and 0.04, respectively. If any of these parameters is bigger, there must be something wrong with your measurement and/or crystal.

20 Postrefine refinements of the orientation matrices of the crystal and two diamonds after integration

21 Each reflection could be inspected on the frames in the case you have doubts about its intensity during data reduction and analysis.

22 Building and viewing reciprocal space Reconstruction of reciprocal space on the basis of the measured frames

23 Twinning at high pressures in the reciprocal space

24 Some parts of the text and one figure were taken from the X- Area manual written by STOE. It is worth spending some time on reading it carefully. X-area is not a black-box software and requires conscious actions from the user.